BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089752.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 35,432,098 number of mapped reads = 29,712,225 (83.86%) number of supplementary alignments = 1,339 (0%) number of secondary alignments = 0 number of mapped bases = 1,406,912,982 bp number of sequenced bases = 1,406,652,306 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,404,679 duplication rate = 11.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9587 >>>>>>> ACTG content number of A's = 434,656,366 bp (30.9%) number of C's = 275,242,819 bp (19.57%) number of T's = 407,863,143 bp (29%) number of G's = 288,684,718 bp (20.52%) number of N's = 205,260 bp (0.01%) GC percentage = 40.09% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 6,195,656 number of insertions = 53,685 mapped reads with insertion percentage = 0.18% number of deletions = 172,750 mapped reads with deletion percentage = 0.58% homopolymer indels = 47.87% >>>>>>> Coverage mean coverageData = 0.4545X std coverageData = 3.5021X There is a 14.68% of reference with a coverageData >= 1X There is a 9.04% of reference with a coverageData >= 2X There is a 6.03% of reference with a coverageData >= 3X There is a 4.14% of reference with a coverageData >= 4X There is a 2.89% of reference with a coverageData >= 5X There is a 2.04% of reference with a coverageData >= 6X There is a 1.46% of reference with a coverageData >= 7X There is a 1.06% of reference with a coverageData >= 8X There is a 0.78% of reference with a coverageData >= 9X There is a 0.57% of reference with a coverageData >= 10X There is a 0.43% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 106183244 0.42600994763419264 6.237626628107782 chr2 243199373 122593999 0.5040884665438673 2.812211471338711 chr3 198022430 85814366 0.4333567970052685 1.5600672362629777 chr4 191154276 100620703 0.5263847877512298 1.9903293879679331 chr5 180915260 91838678 0.5076336733562442 1.7340362245947494 chr6 171115067 71338828 0.4169055902014754 1.7689091771910055 chr7 159138663 80009098 0.5027634170836285 4.261325574107433 chr8 146364022 76336612 0.5215531177463817 8.58538922252693 chr9 141213431 61815548 0.43774552861051863 2.7667511176679502 chr10 135534747 67359561 0.4969910852454685 2.7783257510068746 chr11 135006516 63100496 0.46738852219547683 2.8058015496412056 chr12 133851895 64385353 0.4810193609885015 1.7942729076350687 chr13 115169878 47257634 0.41032980863277463 1.518452609611263 chr14 107349540 43789566 0.4079157302397383 1.726640840093209 chr15 102531392 41087854 0.40073438191495536 1.4863630577439229 chr16 90354753 35137473 0.3888835045567553 1.668039055254669 chr17 81195210 35524684 0.437521917856977 2.0723627889512914 chr18 78077248 40304683 0.5162154665082458 6.0140637658478555 chr19 59128983 22842204 0.3863114642103687 4.065540743259618 chr20 63025520 26646691 0.4227920848570547 1.7101811644641343 chr21 48129895 19509875 0.40535876922233055 2.025102487477623 chr22 51304566 14503502 0.28269417579714057 1.2066616069904013 chrMT 16571 536916 32.400941403656994 21.19869929772202 chrX 155270560 83757182 0.5394273196412764 2.2148264569111515 chrY 59373566 4618232 0.07778262804696622 2.076243375050273